2: CLM BGC

We can use a different I compset: IHistClm60BgcCrop. This experiment is a 20th century transient run using GSWP3 forcing and the biogeochemistry model including crops.

Using query_config again we learn more about this compset:

cd /glade/u/home/$USER/code/my_cesm_code
cime/scripts/query_config --compsets clm | grep "I2000Clm60Sp "

Which will return the following: IHistClm60BgcCrop : HIST_DATM%GSWP3v1_CLM60%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV

Which breaks down into:

Field	Description
HIST	Historical transient starting in 1850
DATM%GSWP3v1	Data Atmosphere Model using GSWP3v1 forcing
CLM60%BGC-CROP	CTSM with clm6_0 physics defaults for big-leaf model with Biogeochemistry and Prognostic Crops
SICE	Stub Sea-ice
SOCN	Stub Ocean
MOSART	MOSART River model
SGLC	Stub Glacier model
SWAV	Stub Ocean Wave model

In biogeochemistry (BGC) mode, CLM grows vegetation rather than prescribing it, computing photosynthesis, allocating carbon to leaves, stems, and roots, and cycling carbon and nitrogen through vegetation, litter, and soil. Leaf area becomes a prognostic result of that carbon balance rather than a satellite input, which makes BGC far better for studying how vegetation responds to change, but costlier, since the carbon pools must be spun up to equilibrium first.

By default, IHIST compsets have a default finidat (initialization file) that they use to initialize the model. We will leave this at default.

Exercise: Run an experimental case with prognostic BGC

Create a case called i.clm.bgc.month3 using the compset IHistClm60BgcCrop at f19_f19_mt233 resolution.

Set the run length to 3 months.

Build and run the model.

Click here for hints

How do I compile?

You can compile with the command:

qcmd -- ./case.build

How do I change the run length to 3 months?

Use xml variables: STOP_OPTION and STOP_N.

How do I check my solution?

When your run is completed, go to the archive directory and navigate to the subdirectory lnd/hist

cd /glade/derecho/scratch/$USER/archive/i.clm.bgc.month3
cd lnd/hist

Check that your archive directory contains the files:

i.fates.year1.clm2.h0a.2000-01.nc  i.fates.year1.clm2.h0i.2000-01.nc
i.fates.year1.clm2.h0a.2000-02.nc  i.fates.year1.clm2.h0i.2000-02.nc
i.fates.year1.clm2.h0a.2000-03.nc  i.fates.year1.clm2.h0i.2000-03.nc
i.fates.year1.clm2.h0a.2000-04.nc  i.fates.year1.clm2.h0i.2000-04.nc
i.fates.year1.clm2.h0a.2000-05.nc  i.fates.year1.clm2.h0i.2000-05.nc
i.fates.year1.clm2.h0a.2000-06.nc  i.fates.year1.clm2.h0i.2000-06.nc
i.fates.year1.clm2.h0a.2000-07.nc  i.fates.year1.clm2.h0i.2000-07.nc
i.fates.year1.clm2.h0a.2000-08.nc  i.fates.year1.clm2.h0i.2000-08.nc
i.fates.year1.clm2.h0a.2000-09.nc  i.fates.year1.clm2.h0i.2000-09.nc
i.fates.year1.clm2.h0a.2000-10.nc  i.fates.year1.clm2.h0i.2000-10.nc
i.fates.year1.clm2.h0a.2000-11.nc  i.fates.year1.clm2.h0i.2000-11.nc
i.fates.year1.clm2.h0a.2000-12.nc  i.fates.year1.clm2.h0i.2000-12.nc

Click here for the solution

Create a new case

Create a new case i.clm.bgc.month3 :

cd /glade/u/home/$USER/code/my_cesm_code/cime/scripts
./create_newcase --case ~/cases/i.clm.bgc.month3 --compset IHistClm60BgcCrop --res f19_f19_mt233 --run-unsupported

Case setup

cd ~/cases/i.clm.bgc.month3
./case.setup

Set run length

Change the run length:

./xmlchange STOP_N=3,STOP_OPTION=nmonths

Note differences between this case and the SP case:

diff env_run.xml ../i.clm.sp.year1/env_run.xml

Check the namelist by running:

./preview_namelists

Change the job queue and account number

If needed, change job queue and account number.

For instance, to run in the queue tutorial and the project number UESM0016:

./xmlchange JOB_QUEUE=tutorial,PROJECT=UESM0016 --force

Change the wallclock time

./xmlchange --subgroup case.run JOB_WALLCLOCK_TIME=01:00:00

Build case

qcmd -- ./case.build

Compare the namelists from the two experiments:

diff CaseDocs/lnd_in ../i.clm.sp.year1/CaseDocs/lnd_in

Submit case

./case.submit

Check the run:

When the run is completed, look into the archive directory for: i.clm.bgc.month3.

Check that your archive directory on derecho (The path will be different on other machines):

cd /glade/derecho/scratch/$USER/archive/i.clm.bgc.month3/lnd/hist

ls 

We will investigate the output in a subsequent exercise.